(Q33869871)

29 July 2017

title

A comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives (English)

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29 July 2017

1 reference

3

Odile Lecompte

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29 July 2017

Julie D Thompson

1

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29 July 2017

Benjamin Linard

series ordinal

2

1 reference

29 July 2017

Olivier Poch

series ordinal

4

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29 July 2017

language of work or name

English

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publication date

31 March 2011

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29 July 2017

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29 July 2017

volume

6

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29 July 2017

issue

3

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29 July 2017

page(s)

e18093

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Creative Commons Attribution 4.0 International

29 July 2017

copyright license

start time

31 March 2011

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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28 July 2018

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28 July 2018

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28 July 2018

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28 July 2018

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28 July 2018

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Establishment of a dog model for the p53 family pathway and identification of a novel isoform of p21 cyclin-dependent kinase inhibitor.

28 July 2018

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Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features

28 July 2018

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28 July 2018

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Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis

28 July 2018

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28 July 2018

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28 July 2018

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28 July 2018

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28 July 2018

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Bioinformatics challenges of new sequencing technology

28 July 2018

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The impact of next-generation sequencing technology on genetics

28 July 2018

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Alignment uncertainty and genomic analysis

28 July 2018

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28 July 2018

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28 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

Automated protein subfamily identification and classification

28 July 2018

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PROMALS: towards accurate multiple sequence alignments of distantly related proteins.

28 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

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28 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

MACSIMS: multiple alignment of complete sequences information management system

28 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

Refining multiple sequence alignments with conserved core regions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

M-Coffee: combining multiple sequence alignment methods with T-Coffee

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences

28 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

A benchmark of multiple sequence alignment programs upon structural RNAs

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

ProbCons: Probabilistic consistency-based multiple sequence alignment

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

MUSCLE: multiple sequence alignment with high accuracy and high throughput

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

Multiple sequence alignment using partial order graphs

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

Protein structure comparison using SAP.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

A comprehensive comparison of multiple sequence alignment programs

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

Profile hidden Markov models

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

SAGA: sequence alignment by genetic algorithm

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

Weighting in sequence space: a comparison of methods in terms of generalized sequences

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

Profile analysis: detection of distantly related proteins

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

Progressive sequence alignment as a prerequisite to correct phylogenetic trees

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

Broad phylogenomic sampling improves resolution of the animal tree of life

28 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018093

Sonic hedgehog mutations identified in holoprosencephaly patients can act in a dominant negative manner.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018093

Species-level diversification of African dwarf crocodiles (Genus Osteolaemus): A geographic and phylogenetic perspective

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018093

3DCoffee: combining protein sequences and structures within multiple sequence alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018093

Phylogenetic assessment of alignments reveals neglected tree signal in gaps

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018093

vALId: validation of protein sequence quality based on multiple alignment data

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018093

Finding novel genes in bacterial communities isolated from the environment

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018093

MEGAN analysis of metagenomic data

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018093

INTREPID--INformation-theoretic TREe traversal for Protein functional site IDentification

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018093

Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018093

The Protein Data Bank: a historical perspective.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018093

Ballast: blast post-processing based on locally conserved segments

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018093

LEON: multiple aLignment Evaluation Of Neighbours

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018093

RASCAL: rapid scanning and correction of multiple sequence alignments.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018093

T-Coffee: A novel method for fast and accurate multiple sequence alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018093

3DM: systematic analysis of heterogeneous superfamily data to discover protein functionalities.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

Analysis and comparison of benchmarks for multiple sequence alignment

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3069049

BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark

29 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21483869

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Towards a reliable objective function for multiple sequence alignments

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21483869

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Secator: a program for inferring protein subfamilies from phylogenetic trees

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21483869

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0018093

1 reference

29 July 2017

0 references

1 reference

29 July 2017

1 reference